[2023-03-17 07:01:49,054] [INFO] DFAST_QC pipeline started.
[2023-03-17 07:01:49,054] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 07:01:49,055] [INFO] DQC Reference Directory: /var/lib/cwl/stg2b222a1a-5e1f-4413-8b37-9a0ba437cbdc/dqc_reference
[2023-03-17 07:01:50,166] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 07:01:50,167] [INFO] Task started: Prodigal
[2023-03-17 07:01:50,167] [INFO] Running command: cat /var/lib/cwl/stg14e9d2f0-d105-48cf-8966-2de176415530/OceanDNA-b22762.fa | prodigal -d OceanDNA-b22762/cds.fna -a OceanDNA-b22762/protein.faa -g 11 -q > /dev/null
[2023-03-17 07:02:08,351] [INFO] Task succeeded: Prodigal
[2023-03-17 07:02:08,351] [INFO] Task started: HMMsearch
[2023-03-17 07:02:08,351] [INFO] Running command: hmmsearch --tblout OceanDNA-b22762/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2b222a1a-5e1f-4413-8b37-9a0ba437cbdc/dqc_reference/reference_markers.hmm OceanDNA-b22762/protein.faa > /dev/null
[2023-03-17 07:02:08,558] [INFO] Task succeeded: HMMsearch
[2023-03-17 07:02:08,558] [INFO] Found 6/6 markers.
[2023-03-17 07:02:08,579] [INFO] Query marker FASTA was written to OceanDNA-b22762/markers.fasta
[2023-03-17 07:02:08,579] [INFO] Task started: Blastn
[2023-03-17 07:02:08,579] [INFO] Running command: blastn -query OceanDNA-b22762/markers.fasta -db /var/lib/cwl/stg2b222a1a-5e1f-4413-8b37-9a0ba437cbdc/dqc_reference/reference_markers.fasta -out OceanDNA-b22762/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 07:02:09,123] [INFO] Task succeeded: Blastn
[2023-03-17 07:02:09,123] [INFO] Selected 20 target genomes.
[2023-03-17 07:02:09,124] [INFO] Target genome list was writen to OceanDNA-b22762/target_genomes.txt
[2023-03-17 07:02:09,133] [INFO] Task started: fastANI
[2023-03-17 07:02:09,133] [INFO] Running command: fastANI --query /var/lib/cwl/stg14e9d2f0-d105-48cf-8966-2de176415530/OceanDNA-b22762.fa --refList OceanDNA-b22762/target_genomes.txt --output OceanDNA-b22762/fastani_result.tsv --threads 1
[2023-03-17 07:02:29,721] [INFO] Task succeeded: fastANI
[2023-03-17 07:02:29,722] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2b222a1a-5e1f-4413-8b37-9a0ba437cbdc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 07:02:29,722] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2b222a1a-5e1f-4413-8b37-9a0ba437cbdc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 07:02:29,729] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 07:02:29,730] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 07:02:29,730] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Botrimarina hoheduenensis	strain=Pla111	GCA_007859815.1	2528000	2528000	type	True	76.3548	52	966	95	below_threshold
Pseudobythopirellula maris	strain=Mal64	GCA_007859945.1	2527991	2527991	type	True	76.11	103	966	95	below_threshold
Botrimarina colliarenosi	strain=Pla108	GCA_007859955.1	2528001	2528001	type	True	75.8821	96	966	95	below_threshold
Posidoniimonas corsicana	strain=KOR34	GCA_007859765.1	1938618	1938618	type	True	75.8803	103	966	95	below_threshold
Lacipirellula limnantheis	strain=I41	GCA_007746075.1	2528024	2528024	type	True	75.849	75	966	95	below_threshold
Botrimarina mediterranea	strain=Spa11	GCA_007753265.1	2528022	2528022	type	True	75.8322	85	966	95	below_threshold
Posidoniimonas polymericola	strain=Pla123a	GCA_007859935.1	2528002	2528002	type	True	75.6708	110	966	95	below_threshold
Lacipirellula parvula	strain=PX69	GCA_009177095.1	2650471	2650471	type	True	75.557	84	966	95	below_threshold
Blastopirellula retiformator	strain=Enr8	GCA_007859755.1	2527970	2527970	type	True	75.4827	50	966	95	below_threshold
Lignipirellula cremea	strain=Pla85_3_4	GCA_007751035.1	2528010	2528010	type	True	75.2518	56	966	95	below_threshold
Bradyrhizobium tropiciagri	strain=SEMIA 6148	GCA_001189845.1	312253	312253	type	True	74.7438	53	966	95	below_threshold
Vineibacter terrae	strain=CC-CFT640	GCA_008039615.1	2586908	2586908	type	True	74.683	73	966	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 07:02:29,730] [INFO] DFAST Taxonomy check result was written to OceanDNA-b22762/tc_result.tsv
[2023-03-17 07:02:29,730] [INFO] ===== Taxonomy check completed =====
[2023-03-17 07:02:29,730] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 07:02:29,730] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2b222a1a-5e1f-4413-8b37-9a0ba437cbdc/dqc_reference/checkm_data
[2023-03-17 07:02:29,731] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 07:02:29,735] [INFO] Task started: CheckM
[2023-03-17 07:02:29,735] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b22762/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b22762/checkm_input OceanDNA-b22762/checkm_result
[2023-03-17 07:03:16,251] [INFO] Task succeeded: CheckM
[2023-03-17 07:03:16,251] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.52%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-17 07:03:16,253] [INFO] ===== Completeness check finished =====
[2023-03-17 07:03:16,254] [INFO] ===== Start GTDB Search =====
[2023-03-17 07:03:16,254] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b22762/markers.fasta)
[2023-03-17 07:03:16,254] [INFO] Task started: Blastn
[2023-03-17 07:03:16,254] [INFO] Running command: blastn -query OceanDNA-b22762/markers.fasta -db /var/lib/cwl/stg2b222a1a-5e1f-4413-8b37-9a0ba437cbdc/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b22762/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 07:03:17,043] [INFO] Task succeeded: Blastn
[2023-03-17 07:03:17,043] [INFO] Selected 13 target genomes.
[2023-03-17 07:03:17,043] [INFO] Target genome list was writen to OceanDNA-b22762/target_genomes_gtdb.txt
[2023-03-17 07:03:17,478] [INFO] Task started: fastANI
[2023-03-17 07:03:17,478] [INFO] Running command: fastANI --query /var/lib/cwl/stg14e9d2f0-d105-48cf-8966-2de176415530/OceanDNA-b22762.fa --refList OceanDNA-b22762/target_genomes_gtdb.txt --output OceanDNA-b22762/fastani_result_gtdb.tsv --threads 1
[2023-03-17 07:03:24,976] [INFO] Task succeeded: fastANI
[2023-03-17 07:03:24,984] [INFO] Found 13 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 07:03:24,984] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCA_016872955.1	s__QWPN01 sp016872955	79.491	399	966	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__QWPN01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016872925.1	s__QWPN01 sp016872925	79.3428	421	966	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__QWPN01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903831155.1	s__QWPN01 sp903831155	79.1076	416	966	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__QWPN01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903958265.1	s__QWPN01 sp903958265	78.9858	319	966	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__QWPN01	95.0	98.26	98.26	0.80	0.80	2	-
GCA_003670825.1	s__QWPN01 sp003670825	78.9148	245	966	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__QWPN01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014192425.1	s__QWPN01 sp014192425	78.839	447	966	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__QWPN01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903919035.1	s__QWPN01 sp903919035	78.8382	347	966	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__QWPN01	95.0	99.57	99.56	0.90	0.89	5	-
GCA_018970605.1	s__QWPN01 sp018970605	78.8098	352	966	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__QWPN01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_010027105.1	s__RGVT01 sp010027105	78.7806	314	966	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__RGVT01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009926295.1	s__RGVT01 sp009926295	78.6435	330	966	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__RGVT01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003669255.1	s__QWPN01 sp003669255	78.6329	221	966	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__QWPN01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003671185.1	s__QWPN01 sp003671185	78.381	362	966	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__QWPN01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009923125.1	s__RGVT01 sp009923125	78.1136	253	966	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__RGVT01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 07:03:24,984] [INFO] GTDB search result was written to OceanDNA-b22762/result_gtdb.tsv
[2023-03-17 07:03:24,984] [INFO] ===== GTDB Search completed =====
[2023-03-17 07:03:24,986] [INFO] DFAST_QC result json was written to OceanDNA-b22762/dqc_result.json
[2023-03-17 07:03:24,986] [INFO] DFAST_QC completed!
[2023-03-17 07:03:24,986] [INFO] Total running time: 0h1m36s